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Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (file contents):
Revision 12 by tim, Tue Sep 28 23:24:25 2004 UTC vs.
Revision 1464 by gezelter, Fri Jul 9 19:29:05 2010 UTC

#	Line 1 | Line 1
1	+	/*
2	+	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	+	*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
12	+	* 2. Redistributions in binary form must reproduce the above copyright
13	+	*    notice, this list of conditions and the following disclaimer in the
14	+	*    documentation and/or other materials provided with the
15	+	*    distribution.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
28	+	* arising out of the use of or inability to use software, even if the
29	+	* University of Notre Dame has been advised of the possibility of
30	+	* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40	+	*/
41	+
42		#include <iostream>
43		#include <fstream>
44		#include <string>
45
5	–	#include "brains/SimSetup.hpp"
46		#include "applications/dump2Xyz/Dump2XYZCmd.h"
47	+	#include "brains/Register.hpp"
48	+	#include "brains/SimCreator.hpp"
49	+	#include "brains/SimInfo.hpp"
50	+	#include "brains/ForceManager.hpp"
51	+	#include "io/DumpReader.hpp"
52	+	#include "utils/simError.h"
53		#include "visitors/AtomVisitor.hpp"
54	+	#include "visitors/ReplacementVisitor.hpp"
55		#include "visitors/CompositeVisitor.hpp"
56		#include "visitors/RigidBodyVisitor.hpp"
57		#include "visitors/OtherVisitor.hpp"
58		#include "visitors/ZconsVisitor.hpp"
59	+	#include "selection/SelectionEvaluator.hpp"
60	+	#include "selection/SelectionManager.hpp"
61	+	#include "visitors/LipidTransVisitor.hpp"
62	+	#include "visitors/AtomNameVisitor.hpp"
63
64	<	using namespace std;
64	>	using namespace OpenMD;
65
66		int main(int argc, char* argv[]){
16	–	gengetopt_args_info args_info;
17	–	string dumpFileName;
18	–	string mdFileName;
19	–	char inFileName[2002];
20	–	string xyzFileName;
21	–	SimInfo* info;
22	–	SimSetup startMe;
23	–	DumpReader* dumpReader;
24	–	ofstream xyzStream;
25	–	int nframes;
26	–	Molecule* mol;
27	–	vector<StuntDouble*> integrableObjects;
28	–	vector<StuntDouble*>::iterator iter;
29	–	vector<RigidBody*> myRigidBodies;
30	–	vector<RigidBody*>::iterator rbIter;
67
68	<	CompositeVisitor* compositeVisitor;
69	<	SSDAtomVisitor* ssdVisitor;
34	<	DefaultAtomVisitor* defaultAtomVisitor;
35	<	LipidHeadVisitor* lipidVisitor;
36	<	RBCOMVisitor* rbCOMVisitor;
37	<	ReplicateVisitor* replicateVisitor;
38	<	WrappingVisitor* wrappingVisitor;
39	<	IgnoreVisitor* ignoreVisitor;
40	<	XYZVisitor* xyzVisitor;
41	<	ZConsVisitor* zconsVisitor;
42	<	PrepareVisitor* prepareVisitor;
43	<	WaterTypeVisitor* waterTypeVisitor;
68	>	//register force fields
69	>	registerForceFields();
70
71	+	gengetopt_args_info args_info;
72	+	std::string dumpFileName;
73	+	std::string xyzFileName;
74	+	bool printVel;
75	+	bool printFrc;
76	+	bool printVec;
77	+	bool printChrg;
78	+
79		//parse the command line option
80	<	if (cmdline_parser (argc, argv, &args_info) != 0)
81	<	exit(1) ;
82	<
83	<
80	>	if (cmdline_parser (argc, argv, &args_info) != 0) {
81	>	exit(1) ;
82	>	}
83	>
84		//get the dumpfile name and meta-data file name
85		if (args_info.input_given){
86		dumpFileName = args_info.input_arg;
87	<	}
88	<	else{
55	<	cerr << "Does not have input file name" << endl;
87	>	} else {
88	>	std::cerr << "Does not have input file name" << std::endl;
89		exit(1);
90		}
91	<	mdFileName = dumpFileName;
59	<	mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md";
60	<
91	>
92		if (args_info.output_given){
93		xyzFileName = args_info.output_arg;
94	<	}
64	<	else{
94	>	} else {
95		xyzFileName = dumpFileName;
96		xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
97		}
98	<
98	>
99		//parse md file and set up the system
100	<	info = new SimInfo();
101	<	startMe.setSimInfo(info );
102	<
73	<	strcpy(inFileName, mdFileName.c_str() );
74	<	startMe.parseFile( inFileName );
75	<
76	<	startMe.createSim();
77	<
100	>	SimCreator creator;
101	>	SimInfo* info = creator.createSim(dumpFileName, false);
102	>	ForceManager* forceMan = new ForceManager(info);
103
104	<	//creat visitor list
105	<	compositeVisitor = new CompositeVisitor();
106	<
107	<	//creat ignore visitor
83	<	if(args_info.ignore_given ||args_info.water_flag){
84	<
85	<	ignoreVisitor = new IgnoreVisitor();
86	<
87	<	for(int i = 0; i < args_info.ignore_given; i++)
88	<	ignoreVisitor->addIgnoreType(args_info.ignore_arg[i]);
89	<
90	<	//ignore water
91	<	if(args_info.water_flag){
92	<	ignoreVisitor->addIgnoreType("SSD");
93	<	ignoreVisitor->addIgnoreType("SSD1");
94	<	ignoreVisitor->addIgnoreType("SSD_E");
95	<	ignoreVisitor->addIgnoreType("SSD_RF");
96	<	ignoreVisitor->addIgnoreType("TIP3P_RB_0");
97	<	ignoreVisitor->addIgnoreType("TIP4P_RB_0");
98	<	ignoreVisitor->addIgnoreType("TIP5P_RB_0");
99	<	ignoreVisitor->addIgnoreType("SPCE_RB_0");
100	<	ignoreVisitor->addIgnoreType("DPD_RB_0");
101	<	}
102	<
103	<	compositeVisitor->addVisitor(ignoreVisitor, 1000);
104	<	}
105	<
106	<	//creat RigidBody Visitor
104	>	//create visitor list
105	>	CompositeVisitor* compositeVisitor = new CompositeVisitor();
106	>
107	>	//create RigidBody Visitor
108		if(args_info.rigidbody_flag){
109	<	rbCOMVisitor = new RBCOMVisitor(info);
109	>	RBCOMVisitor* rbCOMVisitor = new RBCOMVisitor(info);
110		compositeVisitor->addVisitor(rbCOMVisitor, 900);
111		}
112	<
113	<	//compositeVisitor->addVisitor(lipidVisitor, 900);
114	<
114	<	//creat SSD atom visitor
115	<	ssdVisitor = new SSDAtomVisitor(info);
112	>
113	>	//create SSD atom visitor
114	>	SSDAtomVisitor* ssdVisitor = new SSDAtomVisitor(info);
115		compositeVisitor->addVisitor(ssdVisitor, 800);
116	<
117	<	//creat default atom visitor
118	<	defaultAtomVisitor = new DefaultAtomVisitor(info);
116	>
117	>	//create default atom visitor
118	>	DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info);
119		compositeVisitor->addVisitor(defaultAtomVisitor, 700);
120	<
121	<	//creat waterType visitor
122	<	if(args_info.watertype_flag){
123	<	waterTypeVisitor = new WaterTypeVisitor;
124	<	compositeVisitor->addVisitor(waterTypeVisitor, 600);
120	>
121	>	// if we gave the -w option, we want to skip the waters:
122	>	if (!args_info.water_given) {
123	>	//create waterType visitor
124	>	if(args_info.watertype_flag){
125	>	WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor;
126	>	compositeVisitor->addVisitor(waterTypeVisitor, 600);
127	>	}
128	>	}
129	>
130	>	if (args_info.basetype_flag) {
131	>	AtomNameVisitor* atomNameVisitor = new AtomNameVisitor(info);
132	>	compositeVisitor->addVisitor(atomNameVisitor, 550);
133	>	std::cout << compositeVisitor->toString();
134		}
135	<
135	>
136		//create ZconsVisitor
137		if(args_info.zconstraint_flag){
130	–
131	–	zconsVisitor = new ZConsVisitor(info);
138
139	<	if(zconsVisitor->haveZconsMol())
139	>	ZConsVisitor* zconsVisitor = new ZConsVisitor(info);
140	>
141	>	if(zconsVisitor->haveZconsMol()) {
142		compositeVisitor->addVisitor(zconsVisitor, 500);
143	<	else
143	>	} else {
144		delete zconsVisitor;
145	+	}
146		}
138	–
139	–	//creat wrapping visitor
140	–
141	–	if(args_info.periodicBox_flag){
142	–	wrappingVisitor = new WrappingVisitor(info);
143	–	compositeVisitor->addVisitor(wrappingVisitor, 400);
144	–	}
147
148	<	//creat replicate visitor
149	<	if(args_info.repeatX_given > 0 || args_info.repeatY_given > 0 ||args_info.repeatY_given > 0){
150	<	IntVec3 replicateOpt(args_info.repeatX_arg, args_info.repeatY_arg, args_info.repeatZ_arg);
151	<	replicateVisitor = new ReplicateVisitor(info, replicateOpt);
148	>	//create wrapping visitor
149	>
150	>	//if(args_info.periodicBox_flag){
151	>	//  WrappingVisitor* wrappingVisitor = new WrappingVisitor(info);
152	>	//  compositeVisitor->addVisitor(wrappingVisitor, 400);
153	>	//}
154	>
155	>	//create replicate visitor
156	>	if(args_info.repeatX_given > 0 ||
157	>	args_info.repeatY_given > 0 ||
158	>	args_info.repeatY_given > 0) {
159	>	Vector3i replicateOpt(args_info.repeatX_arg,
160	>	args_info.repeatY_arg,
161	>	args_info.repeatZ_arg);
162	>	ReplicateVisitor* replicateVisitor = new ReplicateVisitor(info,
163	>	replicateOpt);
164		compositeVisitor->addVisitor(replicateVisitor, 300);
165		}
166
153	–	//creat xyzVisitor
154	–	xyzVisitor = new XYZVisitor(info);
155	–	compositeVisitor->addVisitor(xyzVisitor, 200);
167
168	<	cout << compositeVisitor->toString();
168	>	//create rotation visitor
169	>	if (args_info.refsele_given&& args_info.originsele_given) {
170	>	compositeVisitor->addVisitor(new LipidTransVisitor(info,
171	>	args_info.originsele_arg,
172	>	args_info.refsele_arg),
173	>	250);
174	>	} else if (args_info.refsele_given || args_info.originsele_given) {
175	>	std::cerr << "Both of --refsele and --originsele should appear by pair"
176	>	<< std::endl;
177	>	exit(1);
178	>	}
179	>
180	>	//create xyzVisitor
181	>	XYZVisitor* xyzVisitor;
182
183	<	//creat prepareVisitor
184	<	prepareVisitor = new PrepareVisitor();
183	>	if (args_info.selection_given) {
184	>	xyzVisitor = new XYZVisitor(info, args_info.selection_arg);
185	>	} else {
186	>	xyzVisitor = new XYZVisitor(info);
187	>	}
188
189	+	if(args_info.velocities_flag){
190	+	printVel = true;
191	+	xyzVisitor->doVelocities(printVel);
192	+	}
193	+	if(args_info.forces_flag){
194	+	printFrc = true;
195	+	xyzVisitor->doForces(printFrc);
196	+	}
197	+	if(args_info.vectors_flag){
198	+	printVec = true;
199	+	xyzVisitor->doVectors(printVec);
200	+	}
201	+	if(args_info.charges_flag){
202	+	printChrg = true;
203	+	xyzVisitor->doCharges(printChrg);
204	+	}
205	+
206	+	compositeVisitor->addVisitor(xyzVisitor, 200);
207	+
208	+	//create prepareVisitor
209	+	PrepareVisitor* prepareVisitor = new PrepareVisitor();
210	+
211		//open dump file
212	<	dumpReader = new DumpReader(dumpFileName.c_str());
213	<	nframes = dumpReader->getNframes();
165	<
166	<	xyzStream .open(xyzFileName.c_str());
212	>	DumpReader* dumpReader = new DumpReader(info, dumpFileName);
213	>	int nframes = dumpReader->getNFrames();
214
215	+	std::ofstream xyzStream(xyzFileName.c_str());
216	+
217	+	SimInfo::MoleculeIterator miter;
218	+	Molecule::IntegrableObjectIterator  iiter;
219	+	Molecule::RigidBodyIterator rbIter;
220	+	Molecule* mol;
221	+	StuntDouble* integrableObject;
222	+	RigidBody* rb;
223	+	Vector3d molCom;
224	+	Vector3d newMolCom;
225	+	Vector3d displacement;
226	+	Mat3x3d hmat;
227	+	Snapshot* currentSnapshot;
228	+
229		for (int i = 0; i < nframes; i += args_info.frame_arg){
230	<	dumpReader->readFrame(info, i);
231	<
232	<	mol = info->molecules;
233	<
230	>	dumpReader->readFrame(i);
231	>
232	>	if (printFrc) forceMan->calcForces();
233	>
234	>	//wrapping the molecule
235	>	if(args_info.periodicBox_flag) {
236	>	currentSnapshot = info->getSnapshotManager()->getCurrentSnapshot();
237	>	for (mol = info->beginMolecule(miter); mol != NULL;
238	>	mol = info->nextMolecule(miter)) {
239	>	molCom = mol->getCom();
240	>	newMolCom = molCom;
241	>	currentSnapshot->wrapVector(newMolCom);
242	>	displacement = newMolCom - molCom;
243	>	for (integrableObject = mol->beginIntegrableObject(iiter);
244	>	integrableObject != NULL;
245	>	integrableObject = mol->nextIntegrableObject(iiter)) {
246	>	integrableObject->setPos(integrableObject->getPos() + displacement);
247	>	}
248	>	}
249	>	}
250		//update atoms of rigidbody
251	<	for(int j = 0; j < info->n_mol; j++){
252	<	myRigidBodies = mol[j].getMyRigidBodies();
253	<
254	<	for(rbIter = myRigidBodies.begin(); rbIter != myRigidBodies.end(); ++rbIter)
255	<	(*rbIter)->updateAtoms();
256	<	}
257	<
251	>	for (mol = info->beginMolecule(miter); mol != NULL;
252	>	mol = info->nextMolecule(miter)) {
253	>
254	>	//change the positions of atoms which belong to the rigidbodies
255	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
256	>	rb = mol->nextRigidBody(rbIter)) {
257	>	rb->updateAtoms();
258	>	if (printVel) rb->updateAtomVel();
259	>	}
260	>	}
261
262		//prepare visit
263	<	for(int j = 0; j < info->n_mol; j++){
264	<	integrableObjects = mol[j].getIntegrableObjects();
265	<
266	<	for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
267	<	(*iter)->accept(prepareVisitor);
268	<	}
269	<
263	>	for (mol = info->beginMolecule(miter); mol != NULL;
264	>	mol = info->nextMolecule(miter)) {
265	>	for (integrableObject = mol->beginIntegrableObject(iiter);
266	>	integrableObject != NULL;
267	>	integrableObject = mol->nextIntegrableObject(iiter)) {
268	>	integrableObject->accept(prepareVisitor);
269	>	}
270	>	}
271	>
272		//update visitor
273		compositeVisitor->update();
192	–
193	–	//visit stuntdouble
194	–	for(int j = 0; j < info->n_mol; j++){
195	–	integrableObjects = mol[j].getIntegrableObjects();
274
197	–	for(iter = integrableObjects.begin(); iter != integrableObjects.end(); ++iter)
198	–	(*iter)->accept(compositeVisitor);
199	–	}
275
276	+	//visit stuntdouble
277	+	for (mol = info->beginMolecule(miter); mol != NULL;
278	+	mol = info->nextMolecule(miter)) {
279	+	for (integrableObject = mol->beginIntegrableObject(iiter);
280	+	integrableObject != NULL;
281	+	integrableObject = mol->nextIntegrableObject(iiter)) {
282	+	integrableObject->accept(compositeVisitor);
283	+	}
284	+	}
285	+
286		xyzVisitor->writeFrame(xyzStream);
287		xyzVisitor->clear();
288
289		}//end for (int i = 0; i < nframes; i += args_info.frame_arg)
290	<
290	>
291		xyzStream.close();
292	<
208	<
292	>	delete prepareVisitor;
293		delete compositeVisitor;
294		delete info;
211	–
212	–
295		}

Comparing trunk/src/applications/dump2Xyz/Dump2XYZ.cpp (property svn:keywords):
Revision 12 by tim, Tue Sep 28 23:24:25 2004 UTC vs.
Revision 1464 by gezelter, Fri Jul 9 19:29:05 2010 UTC

#	Line 0 | Line 1
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